6p9o

Poliovirus 135S-like expanded particle in complex with a monoclonal antibody directed against the N-terminal extension of capsid protein VP1

Method: ELECTRON MICROSCOPY Dmax: 98.5 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

VP1

OrganismNot specified

UniProt P03300

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 180 PDB declaration: 180-meric(180) Consistent with protein copy count Chain 1; UniProt 580–881 Chain 2; UniProt 70–341 Fragment:UNP residues 580-881 Fragment:UNP residues 70-341 VP3 × 60 (Q8QYM4) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;phosphate-buffered saline cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.90 Å
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain 1; UniProt 580–881 Chain 2; UniProt 70–341 Fragment:UNP residues 580-881 Fragment:UNP residues 70-341 VP3 × 1 (Q8QYM4) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;phosphate-buffered saline cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.90 Å
3 Protein heterocomplex Heteromer Protein × 15 PDB declaration: pentadecameric(15) Consistent with protein copy count Chain 1; UniProt 580–881 Chain 2; UniProt 70–341 Fragment:UNP residues 580-881 Fragment:UNP residues 70-341 VP3 × 5 (Q8QYM4) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;phosphate-buffered saline cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.90 Å
4 Protein heterocomplex Heteromer Protein × 18 PDB declaration: octadecameric(18) Consistent with protein copy count Chain 1; UniProt 580–881 Chain 2; UniProt 70–341 Fragment:UNP residues 580-881 Fragment:UNP residues 70-341 VP3 × 6 (Q8QYM4) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;phosphate-buffered saline cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.90 Å
5 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain 1; UniProt 580–881 Chain 2; UniProt 70–341 Fragment:UNP residues 580-881 Fragment:UNP residues 70-341 VP3 × 1 (Q8QYM4) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;phosphate-buffered saline cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.90 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

80 other PDB entries and 246 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POLG_POL1M
Isoform
PDB entities 1, 2
Chains and sequence ranges Author chain 1; PDBConstruct 1–302; UniProt 580–881 Author chain 2; PDBConstruct 1–272; UniProt 70–341

VP3

OrganismNot specified

UniProt Q8QYM4

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 180 PDB declaration: 180-meric(180) Consistent with protein copy count Chain 3; UniProt 342–579 Fragment:UNP residues 342-579 VP1 × 60 (P03300) VP2 × 60 (P03300) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;phosphate-buffered saline cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.90 Å
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain 3; UniProt 342–579 Fragment:UNP residues 342-579 VP1 × 1 (P03300) VP2 × 1 (P03300) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;phosphate-buffered saline cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.90 Å
3 Protein heterocomplex Heteromer Protein × 15 PDB declaration: pentadecameric(15) Consistent with protein copy count Chain 3; UniProt 342–579 Fragment:UNP residues 342-579 VP1 × 5 (P03300) VP2 × 5 (P03300) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;phosphate-buffered saline cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.90 Å
4 Protein heterocomplex Heteromer Protein × 18 PDB declaration: octadecameric(18) Consistent with protein copy count Chain 3; UniProt 342–579 Fragment:UNP residues 342-579 VP1 × 6 (P03300) VP2 × 6 (P03300) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;phosphate-buffered saline cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.90 Å
5 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain 3; UniProt 342–579 Fragment:UNP residues 342-579 VP1 × 1 (P03300) VP2 × 1 (P03300) ELECTRON MICROSCOPY cryo-EM buffer:pH 7.5;phosphate-buffered saline cryo-EM vitrification conditions:Cryogen ETHANE Resolution 2.90 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

2 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q8QYM4_9ENTO
Isoform
PDB entities 3
Chains and sequence ranges Author chain 3; PDBConstruct 1–238; UniProt 342–579

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 6p9o

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6p9o
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6p9o
Deposition date deposition_date2019-06-10
Structure title titlePoliovirus 135S-like expanded particle in complex with a monoclonal antibody directed against the N-terminal extension of capsid protein VP1
Keywords keywordsVirus-antibody complex, poliovirus, cell-entry intermediate, expanded virus, VIRUS; VIRUS
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier29.83
Radius of gyration Rg (electron density) rg_electron29.10
Forward intensity I(0) i086066100.00
Molecular weight molecular_weight74155.0 kDa
Excluded volume excluded_volume93117 ų
Envelope volume envelope_volume116480 ų
Hydration-shell volume shell_volume33839 ų
Envelope diameter envelope_diameter103.4
Shell Rg shell_rg35.58
Envelope Rg envelope_rg29.91
Shape Rg shape_rg29.08
Total Rg total_rg29.78
Total atoms total_atoms10354
Residues n_residues662
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax98.5
Rg (real space) rg_real29.89
Rg uncertainty (real space) rg_real_error0.67
I(0) (real space) i0_real8.6070e+07
I(0) uncertainty (real space) i0_real_error1.3100e+06
Rg (reciprocal space) rg_reciprocal29.86
I(0) (reciprocal space) i0_reciprocal86060000.0000
Solution quality estimate total_estimate0.8856
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary33.5
Skewness Skewness skewness0.409
Kurtosis Kurtosis kurtosis-0.311
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha17420000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.883; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.886

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd6p9o3_
Class classb — All beta proteins
Fold Fold foldb.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamilyb.121.4 — Positive stranded ssRNA viruses
Family Family familyb.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)

CATH v4.4 (3 domains)

Domain ID domain_id6p9o100
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20
Domain ID domain_id6p9o200
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20
Domain ID domain_id6p9o300
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily20

8. Citations (1)

9. Files and Curves (10)